Seems like I'm having a problem loading up the main window in SAM-BA v2.13 after connecting my SAM3U USB CDC device. When I run SAM-BA in GUI mode, everything works fine with a JTAG connection; connection is valid, main window appears after connection. However, the USB CDC virtual COM port never connects when selected as an option.

I've tried to debug this issue by running command scripts to see what's going on. When I try running a command script for the JTAG, I run into a low level initialization issue which causes the applet to not load. When running a command script for USB CDC com port, it seems like the USB serial connection is never found / connected to SAM-BA, thus causing some infinite loop/lock (SAM-BA still shows it's running in my task manager after trying to connect it). I would assume (from reading the documentation) that I do not have to program any additional code for the USB CDC since SAM-BA Bootloader is in SAM3/4 family ROMs.

My two questions are:1) What is the proper command script to load up the applet? This is what I see for one of the examples:

yun wrote:Seems like I'm having a problem loading up the main window in SAM-BA v2.13 after connecting my SAM3U USB CDC device.

You have already been warned that the SAM-BA utility would not interact with your program unless your program emulated the command set.

yun wrote:When I run SAM-BA in GUI mode, everything works fine with a JTAG connection
...
When I try running a command script for the JTAG, I run into a low level initialization issue

Apparently you don't understand the meaning of "everything works", and contradict yourself.

yun wrote:I would assume (from reading the documentation) that I do not have to program any additional code for the USB CDC since SAM-BA Bootloader is in SAM3/4 family ROMs.

You assume incorrectly.
The code in ROM is irrelevant if the processor is busy executing your program.
Read the datasheet for "boot strategies" and the specific procedure to initiate execution of the SAM-BA Monitor program.